scholarly journals CLEPS 1.0: A new protocol for cloud aqueous phase oxidation of VOC mechanisms

2017 ◽  
Vol 10 (3) ◽  
pp. 1339-1362 ◽  
Author(s):  
Camille Mouchel-Vallon ◽  
Laurent Deguillaume ◽  
Anne Monod ◽  
Hélène Perroux ◽  
Clémence Rose ◽  
...  
Keyword(s):  
Gas Phase ◽  
Organic Compounds ◽  
Aqueous Phase ◽  
Water Soluble ◽  
Transfer Scheme ◽  
Chemical Complexity ◽  
Global Rate ◽  
Physico Chemical ◽  
Chemical Scheme ◽  
Phase Chemistry

Abstract. A new detailed aqueous phase mechanism named the Cloud Explicit Physico-chemical Scheme (CLEPS 1.0) is proposed to describe the oxidation of water soluble organic compounds resulting from isoprene oxidation. It is based on structure activity relationships (SARs) which provide global rate constants together with branching ratios for HO⋅ abstraction and addition on atmospheric organic compounds. The GROMHE SAR allows the evaluation of Henry's law constants for undocumented organic compounds. This new aqueous phase mechanism is coupled with the MCM v3.3.1 gas phase mechanism through a mass transfer scheme between gas phase and aqueous phase. The resulting multiphase mechanism has then been implemented in a model based on the Dynamically Simple Model for Atmospheric Chemical Complexity (DSMACC) using the Kinetic PreProcessor (KPP) that can serve to analyze data from cloud chamber experiments and field campaigns. The simulation of permanent cloud under low-NOx conditions describes the formation of oxidized monoacids and diacids in the aqueous phase as well as a significant influence on the gas phase chemistry and composition and shows that the aqueous phase reactivity leads to an efficient fragmentation and functionalization of organic compounds.

scholarly journals Oxidation of low-molecular-weight organic compounds in cloud droplets: development of the Jülich Aqueous-phase Mechanism of Organic Chemistry (JAMOC) in CAABA/MECCA (version 4.5.0)

2021 ◽  
Vol 14 (6) ◽  
pp. 4103-4115
Author(s):  
Simon Rosanka ◽  
Rolf Sander ◽  
Andreas Wahner ◽  
Domenico Taraborrelli
Keyword(s):  
Organic Chemistry ◽  
Gas Phase ◽  
Organic Compounds ◽  
Aqueous Phase ◽  
Phase Transfer ◽  
Cloud Droplets ◽  
Physico Chemical ◽  
Oxygenated Volatile Organic Compounds ◽  
Chemical Scheme ◽  
Selection Of Species

Abstract. The Jülich Aqueous-phase Mechanism of Organic Chemistry (JAMOC) is developed and implemented in the Module Efficiently Calculating the Chemistry of the Atmosphere (MECCA; version 4.5.0). JAMOC is an explicit in-cloud oxidation scheme for oxygenated volatile organic compounds (OVOCs), suitable for global model applications. It is based on a subset of the comprehensive Cloud Explicit Physico-chemical Scheme (CLEPS; version 1.0). The phase transfer of species containing up to 10 carbon atoms is included, and a selection of species containing up to 4 carbon atoms reacts in the aqueous phase. In addition, the following main advances are implemented: (1) simulating hydration and dehydration explicitly; (2) taking oligomerisation of formaldehyde, glyoxal, and methylglyoxal into account; (3) adding further photolysis reactions; and (4) considering gas-phase oxidation of new outgassed species. The implementation of JAMOC in MECCA makes a detailed in-cloud OVOC oxidation model readily available for box as well as for regional and global simulations that are affordable with modern supercomputing facilities. The new mechanism is tested inside the box model Chemistry As A Boxmodel Application (CAABA), yielding reduced gas-phase concentrations of most oxidants and OVOCs except for the nitrogen oxides.

scholarly journals Oxidation of low-molecular weight organic compounds in cloud droplets: development of the JAMOC chemical mechanism in CAABA/MECCA (version 4.5.0gmdd)

2020 ◽  
Author(s):  
Simon Rosanka ◽  
Rolf Sander ◽  
Andreas Wahner ◽  
Domenico Taraborrelli
Keyword(s):  
Gas Phase ◽  
Organic Compounds ◽  
Aqueous Phase ◽  
Phase Transfer ◽  
Chemical Mechanism ◽  
Cloud Droplets ◽  
Physico Chemical ◽  
Chemical Scheme ◽  
Selection Of Species ◽  
Bug Fixes

Abstract. The Jülich Aqueous-phase Mechanism of Organic Chemistry (JAMOC) is developed and implemented in the Module Efficiently Calculating the Chemistry of the Atmosphere (MECCA, version 4.5.0gmdd1). JAMOC is an explicit in-cloud oxidation scheme for oxygenated volatile organic compounds (OVOCs), suitable for global model applications. It is based on a subset of the comprehensive CLoud Explicit Physico-chemical Scheme (CLEPS, version 1.0). The phase transfer of species containing up to ten carbon atoms is included, and a selection of species containing up to four carbon atoms reacts in the aqueous-phase. In addition, the following main advances are implemented: (1) simulating hydration and dehydration explicitly, (2) taking oligomerisation of formaldehyde, glyoxal and methylglyoxal into account, (3) adding further photolysis reactions, and (4) considering gas-phase oxidation of new outgassed species. The implementation of JAMOC in MECCA makes a detailed in-cloud OVOC oxidation model readily available for box as well as for regional and global simulations that are affordable with modern supercomputing facilities. The new mechanism is tested inside the box-model Chemistry As A Boxmodel Application (CAABA), yielding reduced gas-phase concentrations of most oxidants and OVOCs except for the nitrogen oxides. 1 The name of this version indicates that it is used for the interactive discussion in GMDD. If necessary, bug fixes can still be made. We plan to release the final version CAABA/MECCA-4.5.0 together with the final paper in GMD.

Influence of in-cloud oxidation of organic compounds on tropospheric ozone

2021 ◽  
Author(s):  
Simon Rosanka ◽  
Rolf Sander ◽  
Bruno Franco ◽  
Catherine Wespes ◽  
Andreas Wahner ◽  
...  
Keyword(s):  
Gas Phase ◽  
Organic Compounds ◽  
Aqueous Phase ◽  
Phase Transfer ◽  
Sulfur Oxidation ◽  
Box Model ◽  
Atmospheric Models ◽  
Model Studies ◽  
Phase Chemistry ◽  
The Impact

<p>Large parts of the troposphere are affected by clouds, whose aqueous-phase chemistry differs significantly from gas-phase chemistry. Box-model studies have demonstrated that clouds influence the tropospheric oxidation capacity. However, most global atmospheric models do not represent this chemistry reasonably well and are largely limited to sulfur oxidation. Therefore, we have developed the Jülich Aqueous-phase Mechanism of Organic Chemistry (JAMOC), making a detailed in-cloud oxidation model of oxygenated volatile organic compounds (OVOCs) readily available for box as well as for regional and global simulations that are affordable with modern supercomputers. JAMOC includes the phase transfer of species containing up to ten carbon atoms, and the aqueous-phase reactions of a selection of species containing up to four carbon atoms, e.g., ethanol, acetaldehyde, glyoxal. The impact of in-cloud chemistry on tropospheric composition is assessed on a regional and global scale by performing a combination of box-model studies using the Chemistry As A Boxmodel Application (CAABA) and the global atmospheric model ECHAM/MESSy (EMAC). These models are capable to represent the described processes explicitly and integrate the corresponding ODE system with a Rosenbrock solver. </p><p>Overall, the explicit in-cloud oxidation leads to a reduction of predicted OVOCs levels. By comparing EMAC's prediction of methanol abundance to spaceborne retrievals from the Infrared Atmospheric Sounding Interferometer (IASI), a reduction in EMAC's overestimation is observed in the tropics. Further, the in-cloud OVOC oxidation shifts the hydroperoxyl radicals (HO<sub>2</sub>) production from the gas- to the aqueous-phase. As a result, the in-cloud destruction (scavenging) of ozone (O<sub>3</sub>) by the superoxide anion (O<sub>2</sub><sup>-</sup>) is enhanced and accompanied by a reduction in both sources and sinks of tropospheric O<sub>3</sub> in the gas phase. By considering only the in-cloud sulfur oxidation by O<sub>3</sub>, about 13 Tg a<sup>-1</sup> of O<sub>3</sub> are scavenged, which increases to 336 Tg a<sup>-1</sup> when JAMOC is used. With the full oxidation scheme, the highest O<sub>3</sub> reduction of 12 % is predicted in the upper troposphere/lower stratosphere (UTLS). Based on the IASI O<sub>3</sub> retrievals, it is demonstrated that these changes in the free troposphere significantly reduce the modelled tropospheric O<sub>3</sub> columns, which are known to be generally overestimated by global atmospheric models. Finally, the relevance of aqueous-phase oxidation of organics for ozone in hazy polluted regions will be presented.  </p>

scholarly journals Development of a protocol for the auto-generation of explicit aqueous-phase oxidation schemes of organic compounds

2019 ◽  
Vol 19 (14) ◽  
pp. 9209-9239 ◽  
Author(s):  
Peter Bräuer ◽  
Camille Mouchel-Vallon ◽  
Andreas Tilgner ◽  
Anke Mutzel ◽  
Olaf Böge ◽  
...  
Keyword(s):  
Organic Compounds ◽  
Aqueous Phase ◽  
Rate Constants ◽  
Particle Growth ◽  
Chemical Mechanism ◽  
Estimation Methods ◽  
Radical Reactivity ◽  
Chemical Complexity ◽  
Model Studies ◽  
Phase Chemistry

Abstract. This paper presents a new CAPRAM–GECKO-A protocol for mechanism auto-generation of aqueous-phase organic processes. For the development, kinetic data in the literature were reviewed and a database with 464 aqueous-phase reactions of the hydroxyl radical with organic compounds and 130 nitrate radical reactions with organic compounds has been compiled and evaluated. Five different methods to predict aqueous-phase rate constants have been evaluated with the help of the kinetics database: gas–aqueous phase correlations, homologous series of various compound classes, radical reactivity comparisons, Evans–Polanyi-type correlations, and structure–activity relationships (SARs). The quality of these prediction methods was tested as well as their suitability for automated mechanism construction. Based on this evaluation, SARs form the basis of the new CAPRAM–GECKO-A protocol. Evans–Polanyi-type correlations have been advanced to consider all available H atoms in a molecule besides the H atoms with only the weakest bond dissociation enthalpies (BDEs). The improved Evans–Polanyi-type correlations are used to predict rate constants for aqueous-phase NO3 and organic compounds reactions. Extensive tests have been performed on essential parameters and on highly uncertain parameters with limited experimental data. These sensitivity studies led to further improvements in the new CAPRAM–GECKO-A protocol but also showed current limitations. Biggest uncertainties were observed in uptake processes and the estimation of Henry's law coefficients as well as radical chemistry, in particular the degradation of alkoxy radicals. Previous estimation methods showed several deficits, which impacted particle growth. For further evaluation, a 1,3,5-trimethylbenzene oxidation experiment has been performed in the aerosol chamber “Leipziger Aerosolkammer” (LEAK) at high relative humidity conditions and compared to a multiphase mechanism using the Master Chemical Mechanism (MCMv3.2) in the gas phase and using a methylglyoxal oxidation scheme of about 600 reactions generated with the new CAPRAM–GECKO-A protocol in the aqueous phase. While it was difficult to evaluate single particle constituents due to concentrations close to the detection limits of the instruments applied, the model studies showed the importance of aqueous-phase chemistry in respect to secondary organic aerosol (SOA) formation and particle growth. The new protocol forms the basis for further CAPRAM mechanism development towards a new version 4.0. Moreover, it can be used as a supplementary tool for aerosol chambers to design and analyse experiments of chemical complexity and help to understand them on a molecular level.

scholarly journals Development of a protocol for the auto-generation of explicit aqueous-phase oxidation schemes of organic compounds

2019 ◽  
Author(s):  
Peter Bräuer ◽  
Camille Mouchel-Vallon ◽  
Andreas Tilgner ◽  
Anke Mutzel ◽  
Olaf Böge ◽  
...  
Keyword(s):  
Organic Compounds ◽  
Aqueous Phase ◽  
Rate Constants ◽  
Particle Growth ◽  
Estimation Methods ◽  
Radical Reactivity ◽  
Chemical Complexity ◽  
Model Studies ◽  
Aerosol Chamber ◽  
Phase Chemistry

Abstract. This paper presents a new CAPRAM/GECKO-A protocol for mechanism auto-generation of aqueous-phase organic mechanisms. For the development, kinetic data in the literature was reviewed and a database with 464 aqueous-phase reactions of the hydroxyl radical with organic compounds and 130 nitrate radical reactions with organic compounds has been compiled and evaluated. Five different methods to predict aqueous-phase rate constants have been evaluated with the help of the kinetics database: gas-aqueous correlations, homologous series of various compound classes, radical reactivity comparisons, Evans-Polanyi-type correlations, and structure-activity relationships (SARs). The quality of these prediction methods was tested as well as their suitability for automated mechanism construction. Based on this evaluation, SARs form the basis of the new CAPRAM/GECKO-A protocol. Evans-Polanyi-type correlations have been advanced to consider all available H-atoms in a molecule besides the H-atoms with only the weakest bond dissociation enthalpy (BDE). The improved Evans-Polanyi-type correlations are used to predict rate constants for aqueous-phase NO3 + organic compounds reactions. Extensive tests have been performed on essential parameters and highly uncertain parameters with limited experimental data. These sensitivity studies led to further improvements in the new CAPRAM/GECKO-A protocol, but also showed current limitations. Biggest uncertainties were observed in uptake processes and the estimation of Henry's Law coefficients as well as radical chemistry, in particular the degradation of alkoxy radicals. Previous estimation methods showed several deficits, which impacted particle growth. For further evaluation, a mesitylene oxidation experiment has been performed at the aerosol chamber LEAK at high relative humidity conditions and compared to a multiphase mechanism using the MCMv3.2 in the gas phase and a methylglyoxal oxidation scheme of about 600 reactions generated with the new CAPRAM/GECKO-A protocol in the aqueous phase. While it was difficult to evaluate single particle constituents due to concentrations close to the detection limits of the instruments applied, the model studies showed the importance of aqueous-phase chemistry in respect to SOA formation and particle growth. The new protocol forms the basis for further CAPRAM mechanism development towards a new version 4.0. Moreover, it can be used as supplementary tool for aerosol chambers to design and analyse experiments of chemical complexity and help understanding them on a molecular level.

scholarly journals In-cloud oxalate formation in the global troposphere: a 3-D modeling study

2011 ◽  
Vol 11 (12) ◽  
pp. 5761-5782 ◽  
Author(s):  
S. Myriokefalitakis ◽  
K. Tsigaridis ◽  
N. Mihalopoulos ◽  
J. Sciare ◽  
A. Nenes ◽  
...  
Keyword(s):  
Gas Phase ◽  
Aqueous Phase ◽  
Secondary Organic Aerosol ◽  
Transport Model ◽  
Organic Aerosol ◽  
Chemical Oxidation ◽  
Turnover Time ◽  
Water Soluble ◽  
Chemical Production ◽  
Phase Chemistry

Abstract. Organic acids attract increasing attention as contributors to atmospheric acidity, secondary organic aerosol mass and aerosol hygroscopicity. Oxalic acid is globally the most abundant dicarboxylic acid, formed via chemical oxidation of gas-phase precursors in the aqueous phase of aerosols and droplets. Its lifecycle and atmospheric global distribution remain highly uncertain and are the focus of this study. The first global spatial and temporal distribution of oxalate, simulated using a state-of-the-art aqueous-phase chemical scheme embedded within the global 3-dimensional chemistry/transport model TM4-ECPL, is here presented. The model accounts for comprehensive gas-phase chemistry and its coupling with major aerosol constituents (including secondary organic aerosol). Model results are consistent with ambient observations of oxalate at rural and remote locations (slope = 1.16 ± 0.14, r2 = 0.36, N = 114) and suggest that aqueous-phase chemistry contributes significantly to the global atmospheric burden of secondary organic aerosol. In TM4-ECPL most oxalate is formed in-cloud and less than 5 % is produced in aerosol water. About 62 % of the oxalate is removed via wet deposition, 30 % by in-cloud reaction with hydroxyl radical, 4 % by in-cloud reaction with nitrate radical and 4 % by dry deposition. The in-cloud global oxalate net chemical production is calculated to be about 21–37 Tg yr−1 with almost 79 % originating from biogenic hydrocarbons, mainly isoprene. This condensed phase net source of oxalate in conjunction with a global mean turnover time against deposition of about 5 days, maintain oxalate's global tropospheric burden of 0.2–0.3 Tg, i.e. 0.05–0.1 Tg-C that is about 5–9 % of model-calculated water soluble organic carbon burden.

The Impact of the Aqueous Phase Chemistry of HNO4 on Gas Phase Tropospheric Chemistry

2001 ◽  
Vol 32 ◽  
pp. 269-270
Author(s):  
J.E. WILLIAMS ◽  
F.J. DENTENER ◽  
A.R. van den BERG
Keyword(s):  
Gas Phase ◽  
Aqueous Phase ◽  
Tropospheric Chemistry ◽  
Phase Chemistry ◽  
The Impact

scholarly journals Explicit modeling of volatile organic compounds partitioning in the atmospheric aqueous phase

2013 ◽  
Vol 13 (2) ◽  
pp. 1023-1037 ◽  
Author(s):  
C. Mouchel-Vallon ◽  
P. Bräuer ◽  
M. Camredon ◽  
R. Valorso ◽  
S. Madronich ◽  
...  
Keyword(s):  
Organic Matter ◽  
Dissolved Organic Matter ◽  
Water Content ◽  
Gas Phase ◽  
Aqueous Phase ◽  
Water Soluble ◽  
Chemical Mechanism ◽  
Organic Species ◽  
Cloud Water Content ◽  
Isoprene Oxidation

Abstract. The gas phase oxidation of organic species is a multigenerational process involving a large number of secondary compounds. Most secondary organic species are water-soluble multifunctional oxygenated molecules. The fully explicit chemical mechanism GECKO-A (Generator of Explicit Chemistry and Kinetics of Organics in the Atmosphere) is used to describe the oxidation of organics in the gas phase and their mass transfer to the aqueous phase. The oxidation of three hydrocarbons of atmospheric interest (isoprene, octane and α-pinene) is investigated for various NOx conditions. The simulated oxidative trajectories are examined in a new two dimensional space defined by the mean oxidation state and the solubility. The amount of dissolved organic matter was found to be very low (yield less than 2% on carbon atom basis) under a water content typical of deliquescent aerosols. For cloud water content, 50% (isoprene oxidation) to 70% (octane oxidation) of the carbon atoms are found in the aqueous phase after the removal of the parent hydrocarbons for low NOx conditions. For high NOx conditions, this ratio is only 5% in the isoprene oxidation case, but remains large for α-pinene and octane oxidation cases (40% and 60%, respectively). Although the model does not yet include chemical reactions in the aqueous phase, much of this dissolved organic matter should be processed in cloud drops and modify both oxidation rates and the speciation of organic species.

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